pairwiseEqual {alakazam} | R Documentation |
Calculate pairwise equivalence between sequences
Description
pairwiseEqual
determined pairwise equivalence between a pairs in a
set of sequences, excluding ambiguous positions (Ns and gaps).
Usage
pairwiseEqual(seq)
Arguments
seq |
character vector containing a DNA sequences. |
Value
A logical matrix of equivalence between each entry in seq
.
Values are TRUE
when sequences are equivalent and FALSE
when they are not.
See Also
Uses seqEqual for testing equivalence between pairs. See pairwiseDist for generating a sequence distance matrix.
Examples
# Gaps and Ns will match any character
seq <- c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C", E="NTGGG")
d <- pairwiseEqual(seq)
rownames(d) <- colnames(d) <- seq
d
[Package alakazam version 1.3.0 Index]